• Bitter, M. C. et al. Fluctuating selection and global change: a synthesis and review on disentangling the roles of climate amplitude, predictability and novelty. Proc. R. Soc. B 288, 20210727 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Botero, C. A., Weissing, F. J., Wright, J. & Rubenstein, D. R. Evolutionary tipping points in the capacity to adapt to environmental change. Proc. Natl Acad. Sci. USA 112, 184–189 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chevin, L.-M., Lande, R. & Mace, G. M. Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory. PLoS Biol. 8, e1000357 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buffalo, V. & Coop, G. Estimating the genome-wide contribution of selection to temporal allele frequency change. Proc. Natl Acad. Sci. USA 117, 20672–20680 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Clark, R. D. et al. The practice and promise of temporal genomics for measuring evolutionary responses to global change. Mol. Ecol. Resour. https://doi.org/10.1111/1755-0998.13789 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Lynch, M., Wei, W., Ye, Z. & Pfrender, M. E. The genome-wide signature of short-term temporal selection. Proc. Natl Acad. Sci USA 121, e2307107121 (2024).

  • Barton, N. H. & Turelli, M. Evolutionary quantitative genetics: how little do we know? Annu. Rev. Genet. 23, 337–370 (1989).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bertram, J. & Masel, J. Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection. Evolution 73, 883–896 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Hedrick, P. W. Genetic polymorphism in heterogeneous environments: the age of genomics. Annu. Rev. Ecol. Evol. Syst. 37, 67–93 (2006).

    Article 

    Google Scholar
     

  • Messer, P. W., Ellner, S. P. & Hairston, N. G. Can population genetics adapt to rapid evolution? Trends Genet. 32, 408–418 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wittmann, M. J., Bergland, A. O., Feldman, M. W., Schmidt, P. S. & Petrov, D. A. Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift. Proc. Natl Acad. Sci. USA 114, E9932–E9941 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gleason, J. M., Roy, P. R., Everman, E. R., Gleason, T. C. & Morgan, T. J. Phenology of Drosophila species across a temperate growing season and implications for behavior. PLoS ONE 14, e0216601 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boor, G. K. H., Schultz, C. B., Crone, E. E. & Morris, W. F. Mechanism matters: the cause of fluctuations in boom–bust populations governs optimal habitat restoration strategy. Ecol. Appl. 28, 356–372 (2018).

    Article 

    Google Scholar
     

  • Kendall, B. E. et al. Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches. Ecology 80, 1789–1805 (1999).

    Article 

    Google Scholar
     

  • Behrman, E. L., Watson, S. S., O’Brien, K. R., Heschel, M. S. & Schmidt, P. S. Seasonal variation in life history traits in two Drosophila species. J. Evol. Biol. 28, 1691–1704 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Behrman, E. L. & Schmidt, P. How predictable is rapid evolution? Preprint at bioRxiv https://doi.org/10.1101/2022.10.27.514123 (2022).

  • Schmidt, P. S. & Conde, D. R. Environmental heterogeneity and the maintenance of genetic variation for reproductive diapause in Drosophila melanogaster. Evolution 60, 1602–1611 (2006).

    PubMed 

    Google Scholar
     

  • Band, H. T. & Ives, P. T. Correlated changes in environment and lethal frequency in a natural population of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 47, 180–185 (1961).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dobzhansky, T. Genetics of natural populations IX. Temporal changes in the composition of populations of Drosophila pseudoobscura. Genetics 28, 162–186 (1943).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bergland, A. O., Behrman, E. L., O’Brien, K. R., Schmidt, P. S. & Petrov, D. A. Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila. PLoS Genet. 10, e1004775 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Machado, H. E. et al. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 10, e67577 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rudman, S. M. et al. Direct observation of adaptive tracking on ecological time scales in Drosophila. Science 375, eabj7484 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lässig, M., Mustonen, V. & Walczak, A. M. Predicting evolution. Nat. Ecol. Evol. 1, 77 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Charlesworth, B. Evolution in Age-Structured Populations (Cambridge Univ. Press, 1994).

  • Wiberg, R. A. W., Gaggiotti, O. E., Morrissey, M. B. & Ritchie, M. G. Identifying consistent allele frequency differences in studies of stratified populations. Methods Ecol. Evol. 8, 1899–1909 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Corbett-Detig, R. B., Hartl, D. L. & Sackton, T. B. Natural selection constrains neutral diversity across a wide range of species. PLoS Biol. 13, e1002112 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Buffalo, V. & Coop, G. The linked selection signature of rapid adaptation in temporal genomic data. Genetics 213, 1007–1045 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bolnick, D. I., Barrett, R. D. H., Oke, K. B., Rennison, D. J. & Stuart, Y. E. (Non)parallel evolution. Annu. Rev. Ecol. Evol. Syst. 49, 303–330 (2018).

    Article 

    Google Scholar
     

  • Barrett, R. D. H. et al. Linking a mutation to survival in wild mice. Science 363, 499–504 (2019).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Colosimo, P. F. et al. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307, 1928–1933 (2005).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Hoekstra, H. E., Hirschmann, R. J., Bundey, R. A., Insel, P. A. & Crossland, J. P. A single amino acid mutation contributes to adaptive beach mouse color pattern. Science 313, 101–104 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Yeaman, S. et al. Convergent local adaptation to climate in distantly related conifers. Science 353, 1431–1433 (2016).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Dobzhansky, T. Altitudinal and seasonal changes produced by natural selection in certain populations of Drosophila pseudoobscura and Drosophila persimilis. Genetics 33, 158–176 (1948).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hill, W. G. & Robertson, A. The effect of linkage on limits to artificial selection. Genet. Res. 8, 269–294 (1966).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Felsenstein, J. The evolutionary advantage of recombination. Genetics 78, 737–756 (1974).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Neher, R. A. Genetic draft, selective interference, and population genetics of rapid adaptation. Annu. Rev. Ecol. Evol. Syst. 44, 195–215 (2013).

    Article 

    Google Scholar
     

  • Turelli, M. & Barton, N. H. Polygenic variation maintained by balancing selection: pleiotropy, sex-dependent allelic effects and G × E interactions. Genetics 166, 1053–1079 (2004).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aguade, M., Miyashita, N. & Langley, C. H. Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster. Genetics 122, 607–615 (1989).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barton, N. H. Genetic hitchhiking. Phil. Trans. R. Soc. Lond. B 355, 1553–1562 (2000).

    Article 
    CAS 

    Google Scholar
     

  • Begun, D. J. & Aquadro, C. F. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356, 519–520 (1992).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Cai, J. J., Macpherson, J. M., Sella, G. & Petrov, D. A. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 5, e1000336 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Charlesworth, B. & Jensen, J. D. Effects of selection at linked sites on patterns of genetic variability. Annu. Rev. Ecol. Evol. Syst. 52, 177–197 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gillespie, J. H. Junk ain’t what junk does: neutral alleles in a selected context. Gene 205, 291–299 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Macpherson, J. M., Sella, G., Davis, J. C. & Petrov, D. A. Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics 177, 2083–2099 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wittmann, M. J., Mousset, S. & Hermisson, J. Modeling the genetic footprint of fluctuating balancing selection: from the local to the genomic scale. Genetics 223, iyad022 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • Buffalo, V. Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin’s Paradox. eLife 10, e67509 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Coop, G. Does linked selection explain the narrow range of genetic diversity across species? Preprint at bioRxiv https://doi.org/10.1101/042598 (2016).

  • Lewontin, R. C. The Genetic Basis of Evolutionary Change (Columbia Univ. Press, 1974).

  • Levins, R. Evolution in Changing Environments (Princeton Univ. Press, 1968).

  • Stroud, J. T., Moore, M. P., Langerhans, R. B. & Losos, J. B. Fluctuating selection maintains distinct species phenotypes in an ecological community in the wild. Proc. Natl Acad. Sci. USA 120, e2222071120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gingerich, P. D. Rates of evolution: effects of time and temporal scaling. Science 222, 159–161 (1983).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Richardson, J. L., Urban, M. C., Bolnick, D. I. & Skelly, D. K. Microgeographic adaptation and the spatial scale of evolution. Trends Ecol. Evol. 29, 165–176 (2014).

    Article 
    PubMed 

    Google Scholar
     

  • Donihue, C. M. et al. Hurricane-induced selection on the morphology of an island lizard. Nature 560, 88–91 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Campbell-Staton, S. C. et al. Ivory poaching and the rapid evolution of tusklessness in African elephants. Science 374, 483–487 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Exposito-Alonso, M. et al. Genetic diversity loss in the Anthropocene. Science 377, 1431–1435 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Rudman, S. M. et al. Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster. Proc. Natl Acad. Sci. USA 116, 20025–20032 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tilk, S. et al. Accurate allele frequencies from ultra-low coverage Pool-seq samples in evolve-and-resequence experiments. G3 9, 4159–4168 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kessner, D., Turner, T. L. & Novembre, J. Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. Mol. Biol. Evol. 30, 1145–1158 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kofler, R., Pandey, R. V. & Schlötterer, C. PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-seq). Bioinformatics 27, 3435–3436 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     



  • Source link


    administrator